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When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, it is generally a good idea to initialize the model to its steady state, and delay the onset of perturbations such as stimuli (current clamps, synaptic activations etc.) until t (h.t to all you...

You're welcome. A few things I forgot to say-- To see the effects of changing synaptic weight at the times specified in tvec require that h.tstop be set to at least 80 ms (100 would be fine). When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, i...

Interesting problem. You're very close to getting it right. No need to disclose your model cell; it's easy enough to make an isolated soma and use that for interactive software development. from neuron import h, gui # the built-in GUI is very convenient for development and debugging soma = h.Section...

If you're already familiar with Python, why not stick with Python? from neuron import h, gui # or, if you prefer, # from neuron import h # h.load_file('stdgui.hoc') . . . next execute your python code that reads the swc file . . . # then execute the legacy hoc file that does whatever useful stuff yo...

According to Wang et al That's quite a paper. Lots of experiments, lots of results. I think it would be best to have a simulation with rapid onset and washout Drug effects are often represented as simple parameter changes, without regard to the actual time course of application or washout. The mode...

OK, finally I see what you're trying to do. I was fixated on the details of transmitter release itself, thinking that you were concerned with intracellular diffusion of calcium, and went off on a tangent without carefully reading your post from Saturday. My mistake--please put all that aside. The qu...

PDEs are fine as mathematical descriptions of diffusion in a spatially continuous system, but they're not suitable for numerical simulations. You can't just stick a PDE into NMODL. Instead, you must first design a diffusional geometry: a set of "well stirred compartments" whose shapes and ...

The equation I would like to implement is D(\partial^2c)/(\partial x^2)=(cVmax)/(c+Km) Are you sure? coh.mod doesn't contain any variables named c, x, Vmax, or Km. It does have variables called C and km, but C is already completely controlled by other assignment statements, and presumably neither C...

I think this reply might be useful to both of you. is there some documentation or an example of how to implement multithreaded simulation without the NEURON GUI? No. I am aware of one published article that implemented multithreaded simulation without mapping NEURON's "parallel computing" ...

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"As proof of concept" first create a non-parallelized implementation of your model cell, and work with that a bit to make sure that (1) parameter values are correct, and (2) simulation results are what you expected to observe. soma.cm = 9e-3 # membrane capacitance uF/cm2 Experimental evide...

I'm unable to recompile my mod files as there's no NEURON folder in the Applications, and hence no compiler that I can see at least..

Try opening a terminal, cd to the folder that contains your mod files, then at the system prompt execute the command
nrnivmodl

Did that work?

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Same problem Which problem? The first code example from neuron import h from matplotlib import pyplot main = h.Section(name='main') dend = h.Section(name='dend') dend.connect(main) ps = h.PlotShape(False) ps.plot(pyplot) pyplot.show() works for me, although ps.plot(pyplot) does generate this warnin...

If you're interested in simulating anything more than "single shot synaptic activations" of the kind illustrated in figs 1-3 and 7 of V. et al., you'll probably want to use NMODL to implement an event-driven synaptic mechanism that can respond to a series of two or more presynaptic spikes.